Human Cell Atlas

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Human Cell Atlas
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DescriptionThe Human Cell Atlas is a global consortium that is creating detailed maps of the cells in the human body to transform understanding of health and disease.
Organisms Human
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Primary citationRegev, Aviv; et al. (Human Cell Atlas Organizing Committee) (2018). "The Human Cell Atlas White Paper". arXiv: 1810.05192 [q-bio.TO].
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Website www.humancellatlas.org

The Human Cell Atlas is a global project to describe all cell types in the human body, to understand human health and for diagnosing, monitoring, and treating disease. [1] [2]

Contents

The global scientific consortium has a network of more than 3,600 members in 102 countries. [3] The project is making data and resources publicly available, and aims to create an open, ethical and representative atlas to benefit humanity. [1] [4] [5]

As of 2024, the project has mapped approximately 62 million human cells into 18 Biological Networks, which includes cells from vital systems such as the nervous system, lungs, heart, intestine and immune system. [6]

Background and description

The Human Cell Atlas (HCA) consortium was founded in 2016 with the aim of building a biological Atlas of every cell in the human body. [7] The initiative was announced by a consortium after its inaugural meeting in London in October 2016, which established the first phase of the project. [8] [9] Aviv Regev and Sarah Teichmann defined the goals of the project at that meeting, [10] which was convened by the Broad Institute, the Wellcome Trust Sanger Institute and Wellcome Trust. [11] Regev and Teichmann lead the project. [12] [2]

The international consortium released a White Paper in 2017 detailing its plans. The Human Cell Atlas aims to define all human cell types by systematically cataloguing cells based on their type, state, location and lineage using advanced single-cell genomics techniques and computational analysis. [13] [4]

Its scope is to categorize the 37 trillion cells [14] [ citation needed ] of the human body to determine which genes each cell expresses by sampling cells from all parts of the body. [15] This goal has been compared in its ambition to the Human Genome Project, which cataloged the first full human DNA sequence. [16] [17]

The HCA consortium is committed to creating an open, ethical, equitable and representative atlas for humanity that represents and benefits people everywhere. [5] By 2024 it had grown into a global network of more than 3,600 scientists in 102 countries. [3] [18] All aspects of the project will be made "available to the public for free", including software and results. [19] HCA data are freely accessible worldwide through the HCA Data Portal. [3]

The first draft of the Human Cell Atlas is being assembled by researchers in 18 'HCA Biological Networks' mapping individual tissues and organs, including the heart, lung, liver, and immune system. [20] Draft atlases from the HCA Lung [21] , Nervous System [22] , Organoid [23] and Eye Biological Networks have been assembled by HCA researchers collaborating globally with other consortia. [24] In November 2024 the consortium released a collection of studies that are described in the journal Nature as representing 'a significant step towards assembling a first draft atlas'. [6]

Consortium and organisation

The Human Cell Atlas is a global collaborative consortium. It is steered and governed by an Organising Committee [25] of 35 international scientists with diverse areas of expertise, led by Sarah Teichmann and Aviv Regev. A smaller HCA Executive Committees advises on routine tasks. HCA Executive Offices, based across the UK, USA, Japan and Singapore support and coordinate the consortium. [1]

HCA Working Groups for Analysis, Ethics [26] , Equity [5] , Standards and Technology, and Data Ecosystem oversight, harmonize methods and approaches across the consortium [25] .

Regular consortia-wide meetings and local workshops are organised in different locations to enable discussion and collaboration [5] . Regional Networks in Africa, Asia, Latin America and the Middle East, initiated and led by researchers in these areas, help to coordinate efforts to enable the atlas to serve all parts of the world [3] .

Atlasing is organised into 18 HCA Biological Networks, dedicated to mapping and analysing different individual tissues, organs and systems, eg Skin, Gut and Reproduction. Led by experts in their respective biological fields, each Biological Network collaborates with a central computational integration team to achieve an integrated atlas [27] .

Funding

As the Human Cell Atlas is a grass roots-led, global and open scientific project, researchers contributing data and methods to the HCA seek their own funding for their research. [1] Support for their work can come from a huge variety of sources worldwide, for example studies in the 2024 Nature Collection of papers were supported by more than one hundred different funding sources. [28]

In addition, a mix of philanthropic and public funders have initiated HCA funding programmes, focused on specific tissues, data access, methods and representation. These included the Chan Zuckerberg Initiative, [29] [30] the Wellcome Trust, [31] the Helmsley Charitable Trust, [32] the Medical Research Council, [33] the European Union commission, [34] and the British Heart Foundation. [35] The HCA has also received organisational support from the Chan Zuckerberg Initiative, Wellcome, the Klarman Family Foundation, and the Helmsley Charitable Trust, among others. [28]

Some of the first funding to be announced was from the Chan Zuckerberg Initiative (CZI). In October 2017, the Chan Zuckerberg Initiative announced funding for 38 projects related to the Human Cell Atlas. [29] [36] Among this early funding was a grant to the Zuckerman Institute of the Columbia University Medical Center at Columbia University. [19] The grant, titled "A strategy for mapping the human spinal cord with single cell resolution", will fund research to identify and catalogue gene activity in all spinal cord cells. [19] The Translational Genomics Research Institute received a grant to develop a standard for the "processing and storage of solid tissues for single-cell RNA sequencing", compared to the typical practice of relying on the average of sequencing multiple cells. [36] Project home pages are available at the Chan Zuckerberg Initiative's website. [37]

Data

In April 2018, the first data set from the project was released, representing 530,000 immune system cells collected from bone marrow and cord blood. [38]

A research program at the Max Planck Institute of Immunobiology and Epigenetics published an atlas of the cells of the liver, using single-cell RNA sequencing on 10,000 normal cells obtained from nine donors. [39]

The Tabula Sapiens data was published on a dedicated website. [40]

See also

Notes

  1. 1 2 3 4 Regev, Aviv; Teichmann, Sarah; Rozenblatt-Rosen, Orit; Stubbington, Michael; Ardlie, Kristin; Amit, Ido; Arlotta, Paola; Bader, Gary; Benoist, Christophe (2018-10-11), The Human Cell Atlas White Paper, arXiv: 1810.05192 , retrieved 2025-10-02
  2. 1 2 Nowogrodzki 2017.
  3. 1 2 3 4 "The Human Cell Atlas: towards a first draft atlas". www.nature.com. Retrieved 2025-10-02.
  4. 1 2 Regev, Aviv; Teichmann, Sarah A; Lander, Eric S; Amit, Ido; Benoist, Christophe; Birney, Ewan; Bodenmiller, Bernd; Campbell, Peter; Carninci, Piero; Clatworthy, Menna; Clevers, Hans; Deplancke, Bart; Dunham, Ian; Eberwine, James; Eils, Roland (2017-12-05). "The Human Cell Atlas". eLife. 6 e27041. doi: 10.7554/eLife.27041 . ISSN   2050-084X. PMC   5762154 . PMID   29206104. Archived from the original on 2025-08-09.
  5. 1 2 3 4 Amit, Ido; Ardlie, Kristin; Arzuaga, Fabiana; Awandare, Gordon; Bader, Gary; Bernier, Alexander; Carninci, Piero; Donnelly, Stacey; Eils, Roland; Forrest, Alistair R. R.; Greely, Henry T.; Guigo, Roderic; Hacohen, Nir; Haniffa, Muzlifah; Kirby, Emily Sarah (2024-11-20). "The commitment of the human cell atlas to humanity". Nature Communications. 15 (1): 10019. Bibcode:2024NatCo..1510019A. doi:10.1038/s41467-024-54306-x. ISSN   2041-1723. PMC   11579494 .
  6. 1 2 "A 'Wikipedia for cells': researchers get an updated look at the Human Cell Atlas, and it's remarkable". Nature (Editorial). 635 (8039): 523–524. 2024-11-20. Bibcode:2024Natur.635..523.. doi: 10.1038/d41586-024-03754-y . PMID   39567795.
  7. ↑ "The Human Cell Atlas: towards a first draft atlas". www.nature.com. Retrieved 2025-10-02.
  8. ↑ Preidt 2016.
  9. ↑ Yup 2017.
  10. ↑ Sample 2016.
  11. ↑ Wellcome Trust Sanger Institute 2016.
  12. ↑ "Mapping The Human Body – One Cell At a Time". 52 Insights. 2017-08-04. Retrieved 2025-10-02.
  13. ↑ Regev, p. 4.
  14. ↑ Bianconi, Eva; Piovesan, Allison; Facchin, Federica; Beraudi, Alina; Casadei, Raffaella; Frabetti, Flavia; Vitale, Lorenza; Pelleri, Maria Chiara; Tassani, Simone; Piva, Francesco; Perez-Amodio, Soledad; Strippoli, Pierluigi; Canaider, Silvia (2013). "An estimation of the number of cells in the human body". Annals of Human Biology. 40 (6): 463–471. doi:10.3109/03014460.2013.807878. ISSN   1464-5033. PMID   23829164.
  15. ↑ Apple 2018.
  16. ↑ Lindeboom, Rik G. H.; Regev, Aviv; Teichmann, Sarah A. (2021-07-01). "Towards a Human Cell Atlas: Taking Notes from the Past". Trends in Genetics. 37 (7): 625–630. doi: 10.1016/j.tig.2021.03.007 . ISSN   0168-9525. PMID   33879355.
  17. ↑ "A cartography of human histology is in the making". The Economist. ISSN   0013-0613 . Retrieved 2025-10-03.
  18. ↑ Gallagher, James (2024-11-20). "Human Cell Atlas project transforms understanding of human body". BBC News. Retrieved 2025-10-03.
  19. 1 2 3 Silva 2017.
  20. ↑ Parums, Dinah V. (2025-01-01). "Editorial: The Human Cell Atlas. What Is It and Where Could It Take Us?". Medical Science Monitor: International Medical Journal of Experimental and Clinical Research. 30 e947707. doi:10.12659/MSM.947707. ISSN   1643-3750. PMC   11702441 . PMID   39741433.
  21. ↑ Sikkema, Lisa; Ramírez-Suástegui, Ciro; Strobl, Daniel C.; Gillett, Tessa E.; Zappia, Luke; Madissoon, Elo; Markov, Nikolay S.; Zaragosi, Laure-Emmanuelle; Ji, Yuge; Ansari, Meshal; Arguel, Marie-Jeanne; Apperloo, Leonie; Banchero, Martin; Bécavin, Christophe; Berg, Marijn (2023-06-08). "An integrated cell atlas of the lung in health and disease". Nature Medicine. 29 (6): 1563–1577. doi:10.1038/s41591-023-02327-2. ISSN   1546-170X.
  22. ↑ Siletti, Kimberly; Hodge, Rebecca; Mossi Albiach, Alejandro; Lee, Ka Wai; Ding, Song-Lin; Hu, Lijuan; Lönnerberg, Peter; Bakken, Trygve; Casper, Tamara; Clark, Michael; Dee, Nick; Gloe, Jessica; Hirschstein, Daniel; Shapovalova, Nadiya V.; Keene, C. Dirk (2023-10-13). "Transcriptomic diversity of cell types across the adult human brain". Science. 382 (6667) eadd7046. doi:10.1126/science.add7046.
  23. ↑ He, Zhisong; Dony, Leander; Fleck, Jonas Simon; Szałata, Artur; Li, Katelyn X.; Slišković, Irena; Lin, Hsiu-Chuan; Santel, Malgorzata; Atamian, Alexander; Quadrato, Giorgia; Sun, Jieran; Pașca, Sergiu P.; Camp, J. Gray; Theis, Fabian J.; Treutlein, Barbara (2024-11-20). "An integrated transcriptomic cell atlas of human neural organoids". Nature. 635 (8039): 690–698. doi:10.1038/s41586-024-08172-8. ISSN   1476-4687.
  24. ↑ Yanes, Javier (2024-11-20). "More than 3,600 scientists are building a manual of all human cells: 'A Google Maps of biology'". EL PAÍS English. Retrieved 2025-10-03.
  25. 1 2 Rozenblatt-Rosen, Orit; Stubbington, Michael J. T.; Regev, Aviv; Teichmann, Sarah A. (2017-10-26). "The Human Cell Atlas: from vision to reality". Nature. 550 (7677): 451–453. doi:10.1038/550451a. ISSN   1476-4687.
  26. ↑ Kirby, Emily; Bernier, Alexander; Guigó, Roderic; Wold, Barbara; Arzuaga, Fabiana; Kusunose, Mayumi; Zawati, Ma’n; Knoppers, Bartha M. (2024-11-20). "Data sharing ethics toolkit: The Human Cell Atlas". Nature Communications. 15 (1): 9901. doi:10.1038/s41467-024-54300-3. ISSN   2041-1723.
  27. ↑ Rood, Jennifer E.; Wynne, Samantha; Robson, Lucia; Hupalowska, Anna; Randell, John; Teichmann, Sarah A.; Regev, Aviv (January 2025). "The Human Cell Atlas from a cell census to a unified foundation model". Nature. 637 (8048): 1065–1071. doi:10.1038/s41586-024-08338-4. ISSN   1476-4687.
  28. 1 2 "Human Cell Atlas achieves leap in understanding of the human body". www.humancellatlas.org. Retrieved 2025-10-23.
  29. 1 2 zhihao (2017-10-16). "Announcing 38 Grants Supporting The Human Cell Atlas". Chan Zuckerberg Initiative. Retrieved 2025-10-23.
  30. ↑ Damian (2019-06-21). "The Chan Zuckerberg Initiative Awards $68 Million to Support the Growth of the Human Cell Atlas". Chan Zuckerberg Initiative. Retrieved 2025-10-23.
  31. ↑ Aug 2018, News article 9. "Human Cell Atlas gets a boost with first funding from Wellcome" . Retrieved 2025-10-23.{{cite web}}: CS1 maint: numeric names: authors list (link)
  32. ↑ "Helmsley and Chan Zuckerberg Initiative Announce New Grant Opportunities to Support the Growth of Human Cell Atlas". Helmsley Charitable Trust. Retrieved 2025-10-23.
  33. ↑ Abbioui, Abbi (2018-12-09). "Dr. Walid Khaled Awarded Human Cell Atlas Grant from the MRC". www.phar.cam.ac.uk. Retrieved 2025-10-23.
  34. ↑ "EU Funding & Tenders Portal". ec.europa.eu. Retrieved 2025-10-23.
  35. ↑ "Detailed map of the heart provides new insights into heart health and disease". British Heart Foundation. Retrieved 2025-10-23.
  36. 1 2 AZ Big Media 2017.
  37. ↑ from https://www.czbiohub.org/tabula-projects/
  38. ↑ Daley 2018.
  39. ↑ Aizarani et al. 2019.
  40. ↑ The Tabula Sapiens Consortium 2022.

References

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